Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011617.1 Corchorus capsularis cultivar CVL-1 contig11638, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 2953
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:2277 original size:27 final size:27

Alignment explanation


    Indices: 2220--2279  Score: 84
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       2210 AAGTGACCTT

                                     **
       2220 AAAATGACCAAAATGCCCCTAAATGTG
          1 AAAATGACCAAAATGCCCCTAAATGCA

                              * *      
       2247 AAAATGACCAAAATGCCCTTGAATGCA
          1 AAAATGACCAAAATGCCCCTAAATGCA

                  
       2274 AAAATG
          1 AAAATG

       2280 CCCCTAGGTG


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTAAATGCA

Found at i:2687 original size:58 final size:58

Alignment explanation


    Indices: 2530--2815  Score: 197
    Period size: 58  Copynumber: 4.8  Consensus size: 58

       2520 CTCTTGGCTG

                               *                    *              *  
       2530 GAGACCTCAAGCAGGATTTGAAATGAAACAAGATTTTGG-GTTGAAAACTCTCAATTA
          1 GAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGAATTGAAAACTCTCAACTA

                    *                      *   *  *       *       *    
       2587 GAGACCTCGAGCAGGATTTGAAAATGAAACAGGA-CTTAGAATTGATAACTCTCGACTA
          1 GAGACCTCAAGCAGGATTT-AAAATGAAACAAGATTTTGGAATTGAAAACTCTCAACTA

                *  *                       *                           *    
       2645 GAGATCTTAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGAAACTCTCGACTA
          1 GAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGAATTG-----A-AAACTCTCAACTA

                    * **       **                **                 * **    
       2709 GAGACCTCGATTAGGATTTGGAA-G--ACAAGA-TTTAAAATTGAAACAAGAAACTATGGACTA
          1 GAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGAATTG-----A-AAACTCTCAACTA

                                           *               
       2769 GAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAA
          1 GAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGAATTGAAA

       2816 CAAGAAAACT


Statistics
Matches: 179,  Mismatches: 37, Indels: 25
        0.74            0.15        0.10

Matches are distributed among these distances:
  57   33  0.18
  58   52  0.29
  59    1  0.01
  60   44  0.25
  61    6  0.03
  63    7  0.04
  64   36  0.20

ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25


Consensus pattern (58 bp):   
GAGACCTCAAGCAGGATTTAAAATGAAACAAGATTTTGGAATTGAAAACTCTCAACTA

Found at i:2712 original size:64 final size:64

Alignment explanation


    Indices: 2633--2862  Score: 288
    Period size: 60  Copynumber: 3.6  Consensus size: 64

       2623 TAGAATTGAT

                            *  *                                            
       2633 AACTCTCGACTAGAGATCTTAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA

                                * **       **          *     **             
       2697 AACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G--ACAAGA-TTTAAAATTGAAACAAGA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA

                * *                                                          
       2757 AACTATGGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGAA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAG-A

                      *        *           *         
       2822 AACTCTCGACCAGAGACCTTAAGCAGGATTTGAAATGAAAC
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAAC

       2863 TCTCCAACAG


Statistics
Matches: 136,  Mismatches: 25, Indels: 9
        0.80            0.15        0.05

Matches are distributed among these distances:
  60   44  0.32
  61    6  0.04
  63    6  0.04
  64   43  0.32
  65   37  0.27

ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23


Consensus pattern (64 bp):   
AACTCTCGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA

Found at i:2785 original size:60 final size:63

Alignment explanation


    Indices: 2633--2860  Score: 246
    Period size: 64  Copynumber: 3.6  Consensus size: 63

       2623 TAGAATTGAT

                            *  *           *           *     **             
       2633 AACTCTCGACTAGAGATCTTAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGATTTTAAAATTGAAACAAGA

                                * **        *                              
       2697 AACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G-ACAAGA-TTTAAAATTGAAACAAGA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAAAATTGAAACAAGA

                * *                        *           *     **              
       2757 AACTATGGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGAA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATG-AACAAGATTTTAAAATTGAAACAAG-A

                      *        *                   
       2822 AACTCTCGACCAGAGACCTTAAGCAGGATTTGAAATGAA
          1 AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAA

       2861 ACTCTCCAAC


Statistics
Matches: 134,  Mismatches: 25, Indels: 10
        0.79            0.15        0.06

Matches are distributed among these distances:
  60   44  0.33
  61    6  0.04
  63    6  0.04
  64   45  0.34
  65   33  0.25

ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24


Consensus pattern (63 bp):   
AACTCTCGACTAGAGACCTCAAGCAGGATTTGAAATGAACAAGATTTTAAAATTGAAACAAGA

Found at i:2876 original size:65 final size:64

Alignment explanation


    Indices: 2633--2876  Score: 147
    Period size: 65  Copynumber: 3.9  Consensus size: 64

       2623 TAGAATTGAT

                *     *     *  *                         *****              
       2633 AACTCTCGACTAGAGATCTTAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGA
          1 AACTATCGACCAGAGACCTCAAGCAGGATTTAAAATGAAACAATACAACAGAATTGAAACAAGA

                *     *         * **       **          *  **                 
       2697 AACTCTCGACTAGAGACCTCGATTAGGATTTGGAA-G--ACAAGATTTA-A-AATTGAAACAAGA
          1 AACTATCGACCAGAGACCTCAAGCAGGATTTAAAATGAAACAATA-CAACAGAATTGAAACAAGA

                  *   *                                  *****               
       2757 AACTATGGACTAGAGACCTCAAGCAGGATTTAAAATGAAACAATATTTTGGAATTGAAACAAGAA
          1 AACTATCGACCAGAGACCTCAAGCAGGATTTAAAATGAAACAATACAACAGAATTGAAACAAG-A

                *              *           *         ** *          
       2822 AACTCTCGACCAGAGACCTTAAGCAGGATTTGAAATGAAACTCTCCAACAGAATT
          1 AACTATCGACCAGAGACCTCAAGCAGGATTTAAAATGAAACAATACAACAGAATT

       2877 TTGAATCAAA


Statistics
Matches: 140,  Mismatches: 33, Indels: 13
        0.75            0.18        0.07

Matches are distributed among these distances:
  60   41  0.29
  61    6  0.04
  62    4  0.03
  63    6  0.04
  64   40  0.29
  65   43  0.31

ACGTcount: A:0.43, C:0.16, G:0.18, T:0.24


Consensus pattern (64 bp):   
AACTATCGACCAGAGACCTCAAGCAGGATTTAAAATGAAACAATACAACAGAATTGAAACAAGA
Done.